BN9966 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 9.7088e-05 3.3929e-04
Layer 3 9.8948e-05 2.2185e-03
Layer 5 3.4967e-04 2.6217e-03
Layer 2 2.2131e-03 3.3165e-02
WM 2.3394e-03 5.0907e-02
Layer 6 5.6594e-03 3.3973e-02
Layer 1 5.5757e-01 5.2897e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.8145 0.6573
CHGA Layer 4 3.3643 0.6378
TTC9B Layer 4 3.4346 0.6319
SNCG Layer 5 3.0059 0.6274
SH3GL2 Layer 5 3.0117 0.6231
ACTG1 Layer 4 2.4941 0.6230
MOAP1 Layer 4 2.9863 0.6213
TUBB Layer 5 3.0117 0.6207
APBB1 Layer 5 2.3281 0.6206
ANXA6 Layer 3 2.5566 0.6199
FKBP8 Layer 4 2.5664 0.6155
CALY Layer 4 3.2754 0.6121
PRDX2 Layer 4 2.7275 0.6120
ATP5F1B Layer 4 2.6953 0.6106
MYO5A Layer 4 3.3438 0.6096
SNAP91 Layer 5 2.8906 0.6078
SERPINI1 Layer 4 2.9531 0.6077
AP2S1 Layer 4 2.3809 0.6041
PRDX5 Layer 4 2.6221 0.6035
RORB Layer 4 3.9980 0.6009
PFKP Layer 5 3.0859 0.6005
FLOT1 Layer 4 2.3926 0.6004
MDH1 Layer 4 3.2012 0.6000
EIF4G2 Layer 5 2.4395 0.5998
TUBA4A Layer 5 2.6602 0.5982
GRINA Layer 4 2.5811 0.5974
ATP5F1D Layer 4 2.3340 0.5968
COPE Layer 4 2.1289 0.5963
TUBB3 Layer 4 3.0996 0.5952
ATP6V1F Layer 4 2.6191 0.5944
GABRA5 Layer 4 2.6895 0.5942
PI4KA Layer 4 3.2363 0.5940
YPEL3 Layer 4 2.7686 0.5931
TUBB2A Layer 5 3.2500 0.5931
PIN1 Layer 5 2.6133 0.5924
NDRG4 Layer 4 3.1465 0.5913
TMEM14A Layer 5 2.4453 0.5912
STMN3 Layer 3 2.6484 0.5907
ATP5MC3 Layer 4 2.8457 0.5907
SPTAN1 Layer 4 2.7793 0.5896
STX1B Layer 4 2.9727 0.5876
MTCH1 Layer 4 2.6133 0.5866
TUBB4B Layer 4 2.7656 0.5864
GOT1 Layer 4 2.5303 0.5854
B4GAT1 Layer 4 2.5693 0.5851
CNRIP1 Layer 4 2.5840 0.5850
PNMA1 Layer 4 2.9277 0.5846
NUAK1 Layer 4 2.9023 0.5844
DCLK1 Layer 5 2.8652 0.5843
REEP5 Layer 4 2.5215 0.5843

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN9966
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN9966_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9966/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9966/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9966/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9966/report/PD/BN9966_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN9966/report/PD/BN9966_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 11:15:50
  • Number of Processes: 10
  • Spending Time: 0h 4m